
PFRMAT AL                                                                        
TARGET T0119                                                                     
REMARK =========================================================================
AUTHOR 6923-1755-6564                                                           
REMARK Ralf Zimmer, GMD-SCAI,                                                   
REMARK Theo Mevissen, GMD-SCAI,                                                 
REMARK Ingolf Sommer, GMD-SCAI,                                                 
REMARK Thomas Lengauer, GMD-SCAI,                                               
REMARK German National Research Center for Information Technology               
REMARK Institute for Algorithms and Scientific Computing                        
REMARK =========================================================================
METHOD A reduced candidate list is produced via ToPLign [1]                     
METHOD sequence/profile alignments, 123D [2] and RDP [3].                       
METHOD The top scoring candidates from this list and the                        
METHOD corresponding refined alignments have been produced                      
METHOD with RDP [3] using newly derived modifications of                        
METHOD contact capacity [2] and pair interaction potentials.                    
METHOD References:                                                              
METHOD [1] Heinz Mevissen and Ralf Thiele and Ralf Zimmer and Thomas Lengauer:  
METHOD     "Analysis of Protein Alignments -- The software environment ToPLign",
METHOD     GMD, 1994-98.                                                        
METHOD [2] Nick Alexandrov and Ruth Nussinov and Ralf Zimmer:                   
METHOD     "Fast Protein Fold Recognition via Sequence to Structure Alignment   
METHOD     and Contact Capacity Potentials",                                    
METHOD     Pacific Symposium on Biocomputing'96, World Scientific Publ. Co.,    
METHOD     1996, 53--72.                                                        
METHOD [3] Ralf Thiele and Ralf Zimmer and Thomas Lengauer:                     
METHOD     "Recursive Dynamic Programming for Adaptive Sequence                 
METHOD     and Structure Alignment",                                            
METHOD     ISMB'95, C. Rawlings et al. (Eds.), AAAI Press, 384--392.            
METHOD [4] Ralf Thiele and Ralf Zimmer and Thomas Lengauer:                     
METHOD     "Protein Threading by Recursive Dynamic Programming",                
METHOD     JMB,757-779,290,1999                                                 
METHOD [5] Ralf Zimmer and Marko Woehler and Ralf Thiele:                       
METHOD     "New Scoring Schemes for Protein Fold Recognition                    
METHOD     based on Voronoi Contacts",                                          
METHOD     Bioinformatics, 14, 3, 295--308, 1998.                               
METHOD [6] Alexander Zien and Ralf Zimmer and Thomas Lengauer:                  
METHOD     "A simple iterative approach to parameter optimization",             
METHOD     JCB, 2000, in press.                                                 
REMARK =========================================================================
MODEL  2                                                                         
PARENT 1FDR                                                                      
I 106    A     2                                                                 
H 107    D     3                                                                 
H 108    W     4                                                                 
F 109    V     5                                                                 
E 110    T     6                                                                 
G 111    G     7                                                                 
T 112    K     8                                                                 
L 113    V     9                                                                 
A 114    T    10                                                                 
R 115    K    11                                                                 
V 116    V    12                                                                 
E 117    Q    13                                                                 
N 118    N    14                                                                 
L 119    W    15                                                                 
S 120    T    16                                                                 
D 121    D    17                                                                 
S 122    A    18                                                                 
T 123    L    19                                                                 
I 124    F    20                                                                 
T 125    S    21                                                                 
F 126    L    22                                                                 
D 127    T    23                                                                 
I 128    V    24                                                                 
Q 129    H    25                                                                 
L 130    A    26                                                                 
D 131    P    27                                                                 
D 136    V    28                                                                 
I 137    L    29                                                                 
H 138    P    30                                                                 
F 139    F    31                                                                 
L 140    T    32                                                                 
A 141    A    33                                                                 
G 142    G    34                                                                 
Q 143    Q    35                                                                 
Y 144    F    36                                                                 
V 145    T    37                                                                 
N 146    K    38                                                                 
V 147    L    39                                                                 
T 148    G    40                                                                 
L 149    L    41                                                                 
P 150    E    42                                                                 
G 151    I    43                                                                 
T 153    R    47                                                                 
E 154    V    48                                                                 
T 155    Q    49                                                                 
R 156    R    50                                                                 
S 157    A    51                                                                 
Y 158    Y    52                                                                 
S 159    S    53                                                                 
F 160    Y    54                                                                 
S 161    V    55                                                                 
S 162    N    56                                                                 
Q 163    S    57                                                                 
P 164    P    58                                                                 
G 165    D    59                                                                 
N 166    N    60                                                                 
R 167    P    61                                                                 
L 168    D    62                                                                 
T 169    L    63                                                                 
G 170    E    64                                                                 
F 171    F    65                                                                 
V 172    Y    66                                                                 
V 173    L    67                                                                 
R 174    V    68                                                                 
N 175    T    69                                                                 
V 176    V    70                                                                 
P 177    P    71                                                                 
Q 178    D    72                                                                 
G 179    G    73                                                                 
K 180    K    74                                                                 
M 181    L    75                                                                 
S 182    S    76                                                                 
E 183    P    77                                                                 
Y 184    R    78                                                                 
L 185    L    79                                                                 
S 186    A    80                                                                 
Q 188    A    81                                                                 
A 189    L    82                                                                 
K 190    K    83                                                                 
A 191    P    84                                                                 
G 192    G    85                                                                 
D 193    D    86                                                                 
K 194    E    87                                                                 
M 195    V    88                                                                 
S 196    Q    89                                                                 
F 197    V    90                                                                 
T 198    V    91                                                                 
G 199    E    93                                                                 
P 200    A    94                                                                 
F 201    A    95                                                                 
G 202    G    96                                                                 
S 203    F    97                                                                 
F 204    F    98                                                                 
Y 205    V    99                                                                 
L 206    L   100                                                                 
R 207    D   101                                                                 
D 208    E   102                                                                 
V 209    V   103                                                                 
K 210    P   104                                                                 
R 211    H   105                                                                 
P 212    C   106                                                                 
V 213    L   109                                                                 
L 214    W   110                                                                 
M 215    M   111                                                                 
L 216    L   112                                                                 
A 217    A   113                                                                 
G 218    T   114                                                                 
G 219    G   115                                                                 
T 220    T   116                                                                 
G 221    A   117                                                                 
I 222    I   118                                                                 
A 223    G   119                                                                 
P 224    P   120                                                                 
F 225    Y   121                                                                 
L 226    L   122                                                                 
S 227    S   123                                                                 
M 228    I   124                                                                 
L 229    L   125                                                                 
Q 230    R   126                                                                 
V 231    L   127                                                                 
L 232    G   128                                                                 
E 233    K   129                                                                 
Q 234    D   130                                                                 
K 235    L   131                                                                 
G 236    D   132                                                                 
S 237    R   133                                                                 
E 238    F   134                                                                 
H 239    K   135                                                                 
P 240    N   136                                                                 
V 241    L   137                                                                 
R 242    V   138                                                                 
L 243    L   139                                                                 
V 244    V   140                                                                 
F 245    H   141                                                                 
G 246    A   142                                                                 
V 247    A   143                                                                 
T 248    R   144                                                                 
Q 249    Y   145                                                                 
D 250    A   146                                                                 
C 251    A   147                                                                 
D 252    D   148                                                                 
L 253    L   149                                                                 
V 254    S   150                                                                 
A 255    Y   151                                                                 
L 256    L   152                                                                 
E 257    P   153                                                                 
Q 258    L   154                                                                 
L 259    M   155                                                                 
D 260    Q   156                                                                 
A 261    E   157                                                                 
L 262    L   158                                                                 
Q 263    E   159                                                                 
Q 264    K   160                                                                 
K 265    Y   162                                                                 
L 266    E   163                                                                 
P 267    G   164                                                                 
W 268    K   165                                                                 
F 269    L   166                                                                 
E 270    R   167                                                                 
Y 271    I   168                                                                 
R 272    Q   169                                                                 
T 273    T   170                                                                 
V 274    V   171                                                                 
V 275    V   172                                                                 
A 276    S   173                                                                 
H 277    R   174                                                                 
A 278    E   175                                                                 
E 283    T   176                                                                 
R 284    A   177                                                                 
K 285    A   178                                                                 
G 286    G   179                                                                 
Y 287    S   180                                                                 
V 288    L   181                                                                 
T 289    T   182                                                                 
G 290    G   183                                                                 
H 291    R   184                                                                 
I 292    I   185                                                                 
E 293    P   186                                                                 
D 295    A   187                                                                 
W 296    L   188                                                                 
L 297    I   189                                                                 
N 298    E   190                                                                 
G 299    S   191                                                                 
G 300    G   192                                                                 
E 301    E   193                                                                 
V 302    L   194                                                                 
D 303    E   195                                                                 
V 304    V   209                                                                 
Y 305    M   210                                                                 
L 306    L   211                                                                 
C 307    C   212                                                                 
G 308    G   213                                                                 
P 309    N   214                                                                 
V 310    P   215                                                                 
P 311    Q   216                                                                 
M 312    M   217                                                                 
V 313    V   218                                                                 
E 314    R   219                                                                 
A 315    D   220                                                                 
V 316    T   221                                                                 
R 317    Q   222                                                                 
S 318    Q   223                                                                 
W 319    L   224                                                                 
L 320    L   225                                                                 
D 321    K   226                                                                 
T 322    E   227                                                                 
Q 323    T   228                                                                 
G 324    R   236                                                                 
I 325    R   237                                                                 
Q 326    R   238                                                                 
P 327    P   239                                                                 
A 328    G   240                                                                 
N 329    H   241                                                                 
F 330    M   242                                                                 
L 331    T   243                                                                 
F 332    A   244                                                                 
E 333    E   245                                                                 
K 334    H   246                                                                 
F 335    Y   247                                                                 
S 336    W   248                                                                 
TER                                                                              
END                                                                              



